Auckland were pushing hard by fulltime, but were just short of their maiden title.
Chiefs coach Dave Rennie, on hand along with several other Mitre 10 Cup and Super Rugby coaches, must have been pleased seeing two of his franchise provinces win silverware.
Counties Manukau, as they did in 2015, won the second tier Michael Jones Trophy, 35-20 over Bay of Plenty with plenty to spare. Next year they will seek to qualify in the top two of the Chiefs region so they can play for the Graham Mourie Cup. Braces to No 8 Viliami Taulani, who has already played for the Steelers, and centre Salimoni Tukania, were key, while Steelers squad member, first five Orbyn Leger, added six goals.
Taulani scored one try from an 85m burst, looking for all the world like Akira Ioane with his pace and power.
Wellington secured third position in the Premiership with a 31-24 victory over 2015 champions Canterbury. So the big four all made the top four.
New Zealand Rugby general manager rugby Neil Sorensen congratulated the winners.
"What a fantastic way to top a week of outstanding rugby. Congratulations to Waikato and Counties Manukau for their success, and congratulations to all the teams that competed. They put on some highly entertaining footy," said Sorensen.
"This tournament is an important platform to showcase young talent emerging from the provinces, who for the third year converged on Taupo. We are incredibly grateful for the amazing support this event gets every year from the Taupo district."
New Zealand Rugby would also have been, quietly, much happier with the display of the two Auckland teams, who placed second and seventh, a big improvement on the 2015 placings of seventh and last (16th).
Jock Hobbs Memorial national Under 19 tournament
(Owen Delany Park, Taupo)
Day three/finals:
Graham Mourie Cup final (1-2): Waikato 25 (Luke Jacobson try; Matt Lansdown con, 6 pen) Auckland A 22 (Jerry Samania, Loketi Manu, Charles Napa'a tries; Oliver Polson con, Wiseguy Faiane con, pen) HT: 19-7
3-4: Wellington 31 Canterbury 24
5-6: Otago 13 Manawatu 13 (Otago take fifth, having scored two tries to one)
7-8: Auckland B 29 Taranaki 27
Michael Jones Trophy final (9-10): Counties Manukau 35 (Viliami Taulani 2, Salimoni Tukania 2 tries; Orbyn Leger 3 con, 3 pen) Bay of Plenty 20 (Sami Veikoso, Paea Levaka tries; Reece MacDonald 2 con, 2 pen) HT: 12-7
11-12: Tasman 32 Hawke's Bay 20
13-14: North Harbour 27 Northland 0
15-16: Heartland 32 Southland 5